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JAL-4513
Consistent colours assigned to groups generated when subdividing tree
Temporarily configure 3d structure viewer via CLI for a jalview session
optionally display source/provider for structure derived annotations along side the annotation labelJAL-4326
gui controls for configuring bitmap export preferencesJAL-4282
ID width for imported project is affected by changes in font size in User preferences
Configurable bitmap export preferences for height, width and scale factor
user preferences and structure chooser controls for automatically showing PAE annotation row along side pLDDT when loading structure from alphafold, and control secondary structure and temp factor display
Add user properties to control more/all AlignFrame components (esp. Text)
Pymol cannot be opened via Jalview if PymolWin.exe is the configured executable on Windows
Preferences dialog blocks the UI if the web service host is slow to response.
default /etc/jalview_properties allowing debian package-conf to control defaults for new Jalview users
user preference token controlling launch of the news browser (like -nonews argument)
user preference token controlling download of linkout URLs from www.jalview.org/services/identifiers
user preference token controlling download of BIOJSHTML templates
Allow/honour HTTPS proxy configuration for getdown and Jalview services
Allow jalview auto-updates to download to and work from separate user-space directory
Prompt user to install/update external viewer config or gracefully degrade when currently configured viewer is not available, or when importing projects with structure views
Warn user if provided structure viewer location was not able to be used
Extended Structure Preferences GUI for configuring multiple external viewers
Fonts too small in alignment, annotations and Preferences and tabs not appearing correctly in Ubuntu with 4k screen
Enable font anti-aliasing as default settingJAL-3530
All outside pings (e.g. telemetry and JABAWS/Slivka querying) will need to check existing Debian opt-in
Add preference values and gui tab for changing the memory setting at launch
SpinnerNumberModel causing IllegalArgumentException in some circumstances
Protein structure derived annotation tracks not automatically shown when 'add to alignment' preference is enabled (and not available unless it *is* ticked!)
symlink to (e.g.) chimera not recognised as executable
Jalview unresponsive when starting up if local network connection is poor
Make 'Input path' text fields easier to complete for novices
Try harder to locate Chimera executable on windows platforms
Apply consensus logo preferences to group consensus as well
addProperties(String file...) to add fragments Jalview configuration
verify compatibility and migrate jalview / compbio services to https
Fixed id width preference for image output is not respected
Refactor File format suffix export preferences
Sequence limits included in FASTA output regardless of user preference setting
$SEQUENCE_ID$ warning appears on launch when no $SEQUENCE_ID$ setting has been configured
change default visibility for autocalculated annotation rows
User preferences for overview window
allow groovy scripts to be automatically imported on startup
Substitution model configuration UI and user preferences
Support access via Ensembl REST API to GenomeHubs
update dependent configuration beans when Cache.setProperty(..) is called
option to enable/disable 'experimental' options in Jalview's UI
Regular expressions containing '$' are not processed correctly in Link URL templates
Gracefully handle user defined colour file availability
Inform user which template is being used to generate BioJS html if it is different from the latest template
Generic GFF annotation source
Cannot open links in configured browser on OSX
Proxy configuration for individual web services
grid lines separating residues in shaded alignment
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